Substrate recognition by ribonucleoprotein ribonuclease MRP

Esakova, Olga; Perederina, Anna; Quan, Chao; Berezin, Igor; Krasilnikov, Andrey S.

doi:10.1261/rna.2393711

Cited by 24 publications

(41 citation statements)

References 46 publications

(63 reference statements)

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“…4B; Chamberlain et al 1996;Coughlin et al 2008). This is in contrast to the cleavage preference recently determined for RNase MRP, which also does not show extensive requirements for cleaving naked RNA, but has a strong consensus for cytosine at position +4 relative to the cleavage site (Esakova et al 2011).…”

Section: Binding Of Single-stranded Rna To Rnase Pcontrasting

confidence: 78%

Binding and cleavage of unstructured RNA by nuclear RNase P

Marvin

Walker

Fierke³

et al. 2011

RNA

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Ribonuclease P (RNase P) is an essential endoribonuclease for which the best-characterized function is processing the 59 leader of pre-tRNAs. Compared to bacterial RNase P, which contains a single small protein subunit and a large catalytic RNA subunit, eukaryotic nuclear RNase P is more complex, containing nine proteins and an RNA subunit in Saccharomyces cerevisiae. Consistent with this, nuclear RNase P has been shown to possess unique RNA binding capabilities. To understand the unique molecular recognition of nuclear RNase P, the interaction of S. cerevisiae RNase P with single-stranded RNA was characterized. Unstructured, single-stranded RNA inhibits RNase P in a size-dependent manner, suggesting that multiple interactions are required for high affinity binding. Mixed-sequence RNAs from protein-coding regions also bind strongly to the RNase P holoenzyme. However, in contrast to poly(U) homopolymer RNA that is not cleaved, a variety of mixed-sequence RNAs have multiple preferential cleavage sites that do not correspond to identifiable consensus structures or sequences. In addition, pretRNA Tyr , poly(U) 50 RNA, and mixed-sequence RNA cross-link with purified RNase P in the RNA subunit Rpr1 near the active site in ''Conserved Region I,'' although the exact positions vary. Additional contacts between poly(U) 50 and the RNase P proteins Rpr2p and Pop4p were identified. We conclude that unstructured RNAs interact with multiple protein and RNA contacts near the RNase P RNA active site, but that cleavage depends on the nature of interaction with the active site.

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Section: Binding Of Single-stranded Rna To Rnase Pcontrasting

confidence: 78%

Binding and cleavage of unstructured RNA by nuclear RNase P

Marvin

Walker

Fierke³

et al. 2011

RNA

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“…3), where one Pop5/Rpp1 heterodimer bound one RNA molecule (the complex was formed at concentrations of RNA and proteins that were more than an order of magnitude higher than the dissociation constant [below], allowing us to estimate the stoichiometry of the RNA-protein complex). We did not observe the binding of the Pop5/Rpp1 heterodimer to control yeast tRNA or to 140-nt-long (mostly single-stranded) RNA containing a fragment of the internal transcribed spacer 1 (ITS1), a known substrate for RNase MRP (Esakova et al 2011, and references therein; data not shown). Our attempts to perform similar experiments using yeast RNase P RNA did not yield interpretable results, apparently due to misfolding of RNA; the same problem was encountered previously (Perederina et al 2007).…”

Section: Resultsmentioning

confidence: 88%

“…Footprinting studies of RNase MRP and RNase P holoenzymes suggest that the catalytic domain of RNase P and the corresponding domain of RNase MRP have similar structural organizations (Esakova et al 2008). The differences in the substrate specificities of RNases MRP and P (Esakova et al 2011) are likely to be due to the divergence in parts of their RNA components (Fig. 1A,B) and the presence of unique proteins.…”

Section: Introductionmentioning

confidence: 99%

Interactions of a Pop5/Rpp1 heterodimer with the catalytic domain of RNase MRP

Perederina

Khanova

Quan

et al. 2011

RNA

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Ribonuclease (RNase) MRP is a multicomponent ribonucleoprotein complex closely related to RNase P. RNase MRP and eukaryotic RNase P share most of their protein components, as well as multiple features of their catalytic RNA moieties, but have distinct substrate specificities. While RNase P is practically universally found in all three domains of life, RNase MRP is essential in eukaryotes. The structural organizations of eukaryotic RNase P and RNase MRP are poorly understood. Here, we show that Pop5 and Rpp1, protein components found in both RNase P and RNase MRP, form a heterodimer that binds directly to the conserved area of the putative catalytic domain of RNase MRP RNA. The Pop5/Rpp1 binding site corresponds to the protein binding site in bacterial RNase P RNA. Structural and evolutionary roles of the Pop5/Rpp1 heterodimer in RNases P and MRP are discussed.

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“…It was recently shown that RNase MRP has a limited sequence preference for a C at position +4 relative to the site of cleavage (Esakova et al 2011). This preference does not seem to occur with RNase P, which appears to recognize RNA with little regard to primary sequence (Marvin et al 2011).…”

Section: Discussionmentioning

confidence: 99%

Accumulation of noncoding RNA due to an RNase P defect in Saccharomyces cerevisiae

Marvin

Clauder‐Münster²,

Walker

et al. 2011

RNA

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Ribonuclease P (RNase P) is an essential endoribonuclease that catalyzes the cleavage of the 59 leader of pre-tRNAs. In addition, a growing number of non-tRNA substrates have been identified in various organisms. RNase P varies in composition, as bacterial RNase P contains a catalytic RNA core and one protein subunit, while eukaryotic nuclear RNase P retains the catalytic RNA but has at least nine protein subunits. The additional eukaryotic protein subunits most likely provide additional functionality to RNase P, with one possibility being additional RNA recognition capabilities. To investigate the possible range of additional RNase P substrates in vivo, a strand-specific, high-density microarray was used to analyze what RNA accumulates with a mutation in the catalytic RNA subunit of nuclear RNase P in Saccharomyces cerevisiae. A wide variety of noncoding RNAs were shown to accumulate, suggesting that nuclear RNase P participates in the turnover of normally unstable nuclear RNAs. In some cases, the accumulated noncoding RNAs were shown to be antisense to transcripts that commensurately decreased in abundance. Pre-mRNAs containing introns also accumulated broadly, consistent with either compromised splicing or failure to efficiently turn over pre-mRNAs that do not enter the splicing pathway. Taken together with the high complexity of the nuclear RNase P holoenzyme and its relatively nonspecific capacity to bind and cleave mixed sequence RNAs, these data suggest that nuclear RNase P facilitates turnover of nuclear RNAs in addition to its role in pre-tRNA biogenesis.

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Substrate recognition by ribonucleoprotein ribonuclease MRP

Cited by 24 publications

References 46 publications

Binding and cleavage of unstructured RNA by nuclear RNase P

Binding and cleavage of unstructured RNA by nuclear RNase P

Interactions of a Pop5/Rpp1 heterodimer with the catalytic domain of RNase MRP

Accumulation of noncoding RNA due to an RNase P defect in Saccharomyces cerevisiae

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